Brandon King joins Mendeley as Community Liaison

March 31, 2009 Brandon King6 Comments

[Victor:] Completing our trinity of Community Liaison Goodness, may I introduce Brandon King! He is a Ph.D. student in neuroscience at Brown University, doing fascinating research on brain-computer interfaces (so don’t mess with him, or his army of cyborgs will come and get you. No, I just made that up. He’s as nice and funny as they come). We’re excited to have him on our team! Here’s his introduction in his own words:

brandon1 —————————————-

I graduated college 2001, the year that journals were just beginning to become available online. So, for the vast majority of my undergraduate existence, I was forced to do the unthinkable: go to libraries and pull articles from the stacks. “I don’t get it. I’m looking for small bits of constantly updated text, so for my uses, the whole library could be replaced by a web page and a search box.” Of course, this was back when saying you read something on the internet was akin to citing facts from a fictional work.

After spending five years in ‘industry’, I decided to return to academia to continue research on brain-computer interfaces. When I discovered that I could download almost any paper on any topic I could imagine, I was like a kid in a candy store. I could hear my Windows machine cry when the indexer hit my “Papers” folder. As I honed in on my eventual project/thesis topic, I began to amass a big collection of PDFs. “No problem,” I thought. “I’ll just sit down for a whole day at some point and organize it all!”

That was when my papers were numbering around 200. After discovering RSS feeds and launching a blog, that number quickly ballooned up into the thousands. As I type this, there are ~3,700 papers in my library. Yes, it is impossible for me to have read them all, but having read at least the abstracts from each, the interplay of all these ideas and the trends in topics over time have played a major role in shaping my understanding of my field of interest.

Did I mention that none of these PDFs have file names? Well, they didn’t, unless you consider sdarticle(122).pdf to be a useful identifier.

As I started working on my project proposal, I knew I had to find some way to keep this mountain of information in order. It should be easy enough to spend a couple hours tediously searching for each paper in one of those ‘reference manager’ programs, right? Or someone must have come up with a really snazzy web app to take care of references, right? Wrong and wrong. At least that’s what I thought until a member of the Mendeley team brought their program to my attention.

Maybe I dismissed it at first because of the beta moniker or the funny name, but as soon as I installed Mendeley and started to play with it, I was hooked. The hours, nay, days, it saved me made it instantly one of my ‘must have’ programs.

I saw huge potential in Mendeley, and started submitting suggestions and bug reports (it was in version 0.5 at the time) and when Victor came to the States to talk with university librarians, we arranged to meet. I walked away thinking Mendeley could easily be a game changer in the same way online journal access changed research.

We came up with the idea of adding the position I am now starting at because realizing the potential of this awesome tool is only possible by engaging the people that are going to use it. Each lab, each researcher, and each student has their own system of compensating for the near Paleolithic Era reference management tools they have access to. To make Mendeley the most useful program out there, we have to get your feedback on how we can better adapt Mendeley to the way YOU work while at the same time gently nudging people away from the status quo in which reference managing is tedious but necessary. I want to make Mendeley as much a source for creating ideas and new connections between ideas as it is for simply managing references. I think one of the unspoken lessons of research is that you have to stop looking at papers as files or a limited set of ideas, and understand instead how the work fits into the topic of interest as a whole. My hope is that Mendeley will allow researchers to bridge old ideas, inspire new ones, and provide a platform for sharing the information that led them to a novel insight. You know. Small goals, like change everything.

William Gunn joins Mendeley as Community Liaison

March 20, 2009 drgunn5 Comments

Hurray! William Gunn has joined us as Community Liaison! Ricardo Vidal became our first Community Liaison two weeks ago, so with William we have now doubled the brains and talent behind our outreach efforts. William has just completed his Ph.D. on adult stem cells and bone biology at Tulane University. On his blog Synthesis, he has also been writing about open science and social research software. Here’s the story (re-posted from Synthesis) on how he came to join us, in his own words:

—————————-

Reference managers and I have a long history. All the way back in 2004, when I was writing my first paper, my workflow went something like this:

“I need to cite Drs. A, B, and C here. Now, where did I put that paper from Dr. A?” I’d search through various folders of PDFs, organized according to a series of evolving categorization schemes and rifle through ambiguously labeled folders in my desk drawers, pulling out things I knew I’d need handy later. If I found the exact paper I was looking for, I’d then open Reference Manager (v6, I think) and enter the citation details, each in their respective fields. Finding the article, I’d select it and add it to the group of papers I was accumulating.

If it didn’t find it, I’d then go to Pubmed and search for the paper, again entering each citation detail in its field, and then do the required clicking to get the .ris file, download that, then import that into Reference Manager. Then I’d move the reference from the “imported files” library to my library, clicking away the 4 or 5 confirmation dialogs that occurred during this process. On to the next one, which I wouldn’t be able to find a copy of, and would have to search Pubmed for, whereupon I’d find more recent papers from that author, if I was searching by author, or other relevant papers from other authors, if I was searching by subject. Not wanting to cite outdated info, I’d click through from Pubmed to my school’s online catalog, re-enter the search details to find the article in my library’s system, browse through the system until I found a link to the paper online, download the PDF and .ris file (if available), or actually get off my ass and go to the library to make a copy of the paper.

As I was reading the new paper from the Dr. B, I’d find some interesting new assertion, follow that trail for a bit to see how good the evidence was, get distracted by a new idea relevant to an experiment I wanted to do, and emerge a couple hours later with an experiment partially planned and wanting to re-structure the outline for my introduction to incorporate the new perspective I had achieved. Of course, I’d want to check that I wouldn’t be raising the ire of a likely reviewer of the paper by not citing the person who first came up with the idea, so I’d have some background reading to do on a couple of likely reviewers. The whole process, from the endless clicking away of confirmation prompts to the fairly specific Pubmed searches which nonetheless pulled up thousands of results, many of which I wasn’t yet aware, made for extraordinarily slow going. It was XKCD’s wikipedia problem writ large.Read More »

Be afraid… it's the Attack of the Zombie Coders!

March 18, 2009 victorhenning

Yesterday we posted a photo of the Mendeley Team on our roof terrace, trying to jump simultaneously to celebrate our Plugg.eu win:

Always vigilant, our very own Dr. Ridout said he “noticed something creepy” about the photo. Thanks to his keen perception and a few very subtle, barely noticeable image enhancements, he was able to uncover the harrowing truth! Here is the unsettling evidence, not suitable for minors:

THEY’RE SHUFFLING TO A COMPUTER NEAR YOU!

We won the Plugg Conference Start-Up Rally! Here's how it went..

March 17, 2009 victorhenning7 Comments

We’re still in a state of disbelief that we won the start-up pitching competition at Plugg.eu! We honestly thought we’d go to Brussels and not many people would care about this peculiar research software start-up, with so many other more mainstream-focused start-ups (movies, telecommunication, advertising…) in the running. But I’m getting ahead of myself – here’s the full story:

Even before the conference started, Jan and I had managed to get ourselves confused. In true (and unwise) start-up fashion, we had planned on finishing our presentation the night before the pitch, i.e. the Wednesday on which we would be leaving to Brussels. The weekend before, I had been visiting my girlfriend in Hamburg. On Monday morning, when I was still in Hamburg, Jan called me on my mobile:

Jan: Uh, you know, I just found out we have to hand in our Plugg presentations at noon today.

Victor: At noon… today?

Jan: Today.

Victor: That’s in about 3 hours! That’s not good!

Jan: Right.

Victor: And we have this other conference call now…

Jan: … so we’ll have to do the presentation after that.

Victor: Riiiiight…

So we had to figure out a way to finish both the two-minute pitch and the ten-minute presentation (which would only be needed if we were elected as one of the three finalists) within two hours. What we decided to do was: Take the presentation we usually give to universities and libraries, take some slides from the pitch we used to give to VCs when we were looking for funding, mix them up well, hope it’s coherent.

On Wednesday afternoon, we boarded the EuroStar to Brussels. Later that day, all the start-up rally participants were invited to a nice dinner (I forgot which hotel it was). We returned to our own hotel in the centre of Brussels shortly before midnight and thought it would be a good time for me to start practicing the two-minute pitch. Despite (or because of) the couple glasses of wine I had, it went quite well on the second or third try, so we called it a day.

After a little more than five hours sleep, in which Jan and I had to fight over the same blanket, we got up again and made our way to the Plugg conference. There were some pastries for breakfast, which I couldn’t eat due to my egg allergy, so coffee was all I got. Lack of preparation, lack of sleep, lack of breakfast and an overdose of caffeine then summed up to a pretty jittery feeling before I was finally called on stage for the pitch.

Actually, it was Jan who was called on stage due to a mix-up, so I opened our pitch with the odd choice of “I’m actually not Jan, but that’s not important.” I thought it didn’t get better from there: The jittery feeling had developed into a first-rate nervousness, the slide clicker didn’t work properly and skipped slides, and the timer which told me how many seconds I had left was only shown intermittently, blacking out the screen on which I could view my slides. Here’s me stumbling through it (at least that’s what it felt like to me):

http://vimeo.com/moogaloop.swf?clip_id=3603806&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1
Startups Rally – Part 1.3 – Elevator Pitches from Plugg Conference on Vimeo.

So after I returned to my seat, I said to Jan: “I completely borked that one, didn’t I?”, to which he responded “Weeell… maybe not completely.” We both thought that that had been it – at least we wouldn’t have to worry about the ten-minute pitch in the afternoon, which we hadn’t practiced at all.

Imagine our surprise when the audience reaction on Twitter wasn’t that bad, and some people even congratulated us on a good pitch during the lunch break! I concluded that they had probably seen someone else’s pitch. However, it got even weirder when the jury announced the three finalists: Jinni, Myngle, and us! After Jan and I had calmed down again, my first thought was: “Ok, I should better think about what to say.”

So I was still a little nervous when I was called Jan was called to the stage for the final presentation again. Here’s the result:

http://vimeo.com/moogaloop.swf?clip_id=3633550&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1
Startups Rally – Part 2.2 – Final Pitches from Plugg Conference on Vimeo.

I felt the talk, again, was ok, but far from great – but the Q&A at the end went reasonably well. Yet to me, Marina’s/Myngle’s talk seemed much smoother, and after they had won the Audience Award (congrats to Myngle!), I was sure that they’d win the jury vote as well.

As the overall winner was being announced, I can’t even express how STUNNED Jan and I were when the Mendeley logo was projected onto the screen! WOOO-HOOO! The next few minutes are a blur of hugging, jumping up and down, and celebrating. Not only had we won the vote of the jury, composed of acclaimed VCs and academics, but also €2,000 credit at Amazon Web Services and a brand-new X2250 server from Sun!

And here’s a funny aside: Just three hours earlier, sitting next to me in the audience, Jan had ordered a new server from Dell because we were badly in need of a new one. Guess who we had to call right after our win to cancel the order?

What followed was a pretty fabulous evening in Brussels! Jan and I were too exhausted to party – instead, we just went to a nice little restaurant in Ixelles (close to where I studied back in 2002) and had a quiet dinner in excellent spirits. Merci Bruxelles! Photos from our trip can be found on our Flickr account.

P.S. Thank you to everyone who made this such a memorable event for us: First of all, the entire Mendeley Team without which none of this would be possible; the jury and the audience, the Plugg conference organizers and sponsors, and all the great people we met and talked to – you know who you are…

P.P.S. Here are some photos of the Mendeley Team celebrating the win on our roofterrace in the sunshine:

Fig. 1: Nerds trying to jump at the same time, failing badly

Fig. 2: Standing still works better

Mendeley Desktop 0.6.3

March 12, 2009 Mike Arthur

The moons have once more aligned and we would like to announce the release of a new version of Mendeley Desktop for your software-using pleasure, including the Word plugin.

Thank-you all for your feedback, it’s really helped to shape this release. If you have any problems with Mendeley or you wish to request cool new stuff for us to add please visit our feedback forum, which is accessible through the Help menu.

New Features

PDF file organisation and renaming tool
Automatic extraction and retrieval of metadata for ArXiv papers
Lookup metadata for documents based on their PubMed ID
Invite other researchers who are not Mendeley contacts to join Shared Document Groups from within the program
Store and sync paper abstracts
Link to your Mendeley profile and online library in Mendeley Desktop

Improvements to Existing Features:

Author extraction improvements in the PDF importer – This release lays the groundwork for future metadata extraction improvements
Faster startup with large libraries
Reduce the number and duration of pauses during synchronisation, especially with large libraries
Improved auto-completion of authors
Allow deletion of documents in Recently Added and Ungrouped views
Display the number of documents in groups next to the group name
Warn the user if they accidentally try to add papers to ‘My Publications’ if they do not appear in the author list for that paper
Show number of PDFs uploaded/downloaded from Mendeley Web while syncing
More informative progress updates during PDF import
Import tags from Bibtex, RIS files
Export tags to Bibtex files
Word plugin installer integrated into Mendeley Desktop (Tools menu)
More citation styles for citation view and Word plugin
Bibliographies in Word plugin have hanging indents for certain styles
Various improvements to citation formatting

Bug Fixes (General)

More robust synchronisation – fixed many bugs which could occur whilst syncing
Various citation formatting improvements
Various Bibtex import fixes – Bibtex files generated by Google Scholar and Web of Science now import correctly
Support RefWorks-generated RIS files
Prevent pasting rich text into metadata fields which do not support it
Use case insensitive sorting in fields list and table view
Strip XML tags when exporting notes to Bibtex or RIS
Fix ‘Save’ button not being enabled when viewing un-corrected metadata until at least one of the fields had been changed
Removed in-line editing in table view as it was accidentally activated too easily
Fixed problems entering ISBN, ISSN information
Made several error messages less scary
Fix current article selection being lost when sorting library
Fixed imported documents being added to different groups if the user changed the selection while the import was in progress
Fixed searching for exact phrases using quotation marks
Stop trying to upload PDF files if account quota is reached
Fixed bug causing scary message about UUID clash

Bug Fixes (Windows)

Fixed crashes when importing certain PDFs on Windows
File auto-renamer could create file names which were too long on Windows

Bug Fixes (Mac)

Fixed crash during online metadata retrieval when importing PDFs
Now works on OSX systems which have Qt/KDE installed (fix possible crash on startup)

Bug Fixes (Linux)

Make Ubuntu package require the Qt 4 SQLite plugin
Now compatible with Qt 4.5

Ricardo Vidal joins Mendeley as Community Liaison

March 4, 2009 victorhenning7 Comments

Today we can announce another bit of news that makes us very happy! For a while, we’ve been looking for help in better engaging the academic community, involving it more in our roadmap decisions, and also understanding the needs of life scientists better. Consider this: We’re all social scientists, computer scientists and engineers here at Mendeley HQ, and we couldn’t pick this guy PubMed out of a police lineup.

Ok, I’m exaggerating (our next release of Mendeley Desktop, due next week, will enable manual PubMed ID lookups, and the next release after that will do PubMed lookups for all your PDFs automatically). However, the help we’ve been looking for has now arrived in the congenial, talented and Portuguese shape of Ricardo Vidal, author of My Biotech Life! You can see his picture on the top right, and his “silly microbe” design down on the left.

Ricardo will become our first “Community Liaison”. While continuing on with his graduate studies, he’ll also devote a few hours each week to interacting with other researchers on the blogosphere, Twitter, and other social media on Mendeley’s behalf.

I first came across Ricardo’s blog around June last year, because he had written an article about his research paper management needs. So I left a comment pointing him to Mendeley, and he asked for a few invitation codes to the then-ongoing private beta for his readers. We were happy to give him twenty, which were gone only hours after Ricardo offered them on his blog! We loosely stayed in touch ever since and were grateful for the continued support he’s given us over time.

For this announcement, I asked Ricardo to briefly introduce himself and describe why he decided to join us as a Community Liaison and what his hopes for Mendeley were. Here are his answers:

Introduction
Let’s see… I’m currently concluding my Master of Engineering degree in Biological Engineering at the University of Algarve, in Southern Portugal. I’ve been blogging since 2006 at My Biotech Life and am also the co-founder of the DNA Network, a leading network of DNA-related blogs. I also produce (sometimes silly) biotech graphics and logos from time to time.

Why I joined
Besides the fact that I am terrible at keeping my digital papers in order on my laptop or online, I believe that Mendeley represents not only a two-in-one solution for research paper management but also comprises another aspect that I consider of extreme importance, networking. The ability to contact and share your work with researchers alike is invaluable.

Hope/vision for Mendeley
Looking at the progress that has taken place since Mendeley’s launch, I can only hope that things keep evolving as they are now. The roadmap looks promising and the user feedback can only make it a better piece of software as time goes by.

As it has been stated, I also envision Mendeley to become the “Last.fm for Research Papers” where user statistics and networking play a vital part in research, by providing easier access and interaction to scientific information.

Are you looking for a research job?

Mendeley among the 20 finalists of Plugg.eu's European Startup competition

March 2, 2009 Jan Reichelt1 Comment

And again some great news – Mendeley is among the 20 finalists of Plugg.eu’s European startup competition, organized by TechCrunch writer Robin Wauters (TechCrunch coverage here)! In total, 133 companies applied, with a jury of VCs and entrepreneurs selecting the finalists. The whole event sounds really promising, with a number of interesting speakers from Google, Sun, Dopplr, Tapulous, or Atlas Ventures.

It’s actually the first startup competition in which we’ve participated! Also, it’s nice to see the European startup scene growing further, and I’m looking forward to meeting the other entrepreneurs. So we’ll hop over to Brussels next week and try to give our best in the planned elevator pitch presentation. If you will be there as well, it would be great to meet you!

Addition from Victor:

And I’m really excited about visiting Brussels again… I spent a few very happy months there in 2002 as an Erasmus student at the Université Libre de Bruxelles. I lived in Rue Edith Cavell in Uccle, close to the Bois de la Cambre with its pretty parks and lakes. I mostly spent my time with a polyglot bunch of French, Italian, Portuguese, Swedish and Danish exchange students, who would meet almost every night at Le Tavernier or one of the cafés on Place Saint-Géry… from where we’d go for midnight french fries avec sauce piri-piri at the stall behind La Bourse. Good times!

Mendeley Blog

Month: March 2009